The High-throughput Molecular Profiling Core provides the global genomic and proteomic measurements that are essential for applying a systems biology approach to defining innate and adaptive immune responses to virus infection. Each of the Research Projects will provide numerous biological samples for high-throughput analysis. The majority of samples will come from Collaborative Cross lines infected with SARS-CoV (Project 1), influenza virus (Project 2), or West Nile virus (Projects 3 and 4). Global gene expression data obtained from these samples will provide the basis for expression quantitative trait loci (eQTL) analysis and gene expression network inference. Information obtained from these analyses will be indispensable for the identification of genes and gene networks that regulate virus-induced inflammation and innate and adaptive immune responses. The Specific Aims of the Core are as follows: Aim 1: Provide microarray-based gene expression profiling to support expression quantitative trait loci (eQTL) analysis and gene expression network inference in the Collaborative Cross. The Core will provide large-scale sample handling, RNA isolation, quality control, and transcriptomic measurements. Gene expression profiling will be performed using the Affymetrix GeneChip Mouse Gene 1.1 ST Array. Gene expression data will be provided to the Bioinformatics Core, which will be responsible for data management, functional interpretation of gene expression changes, and internal and public data dissemination. eQTL analysis and gene expression network inference will be conducted by the Systems Immunogenetics Core. Aim 2: Provide targeted next generation sequencing and proteomic profiling on select Collaborative Cross lines. The Core will provide additional high-throughput transcriptomic and proteomic measurements on a small number of select Collaborative Cross lines identified by Program investigators as having immune response phenotypes of particular interest. This will include next-generation sequencing to identify and quantify large and small noncoding RNAs and quantitative proteomic approaches for protein abundance profiling, targeted proteomics, or the analysis of specific post-translational modifications.